[phenixbb] amazing good statistics
Simon Kolstoe
s.kolstoe at ucl.ac.uk
Wed Apr 11 07:55:19 PDT 2012
Is there an equivalent of phenix.r_factor_statistics for other parameters like RMSD bond angles/lengths? I note you can get histograms in the GUI version of polygon but only when you input a pdb file for validation.
Thanks,
Simon
On 3 Apr 2012, at 18:41, Pavel Afonine wrote:
> Hi Christian,
>
> this is kind of Rwork/Rfree that you would get if you take a very high resolution structure, may be 1.2-1A and higher, cut the data off at 2.2A, and refine it again.
> So one explanation is that your crystals could probably diffract to a higher resolution...
>
> The command
>
> phenix.r_factor_statistics 2.2
>
> gives typical R-factors at around 2.2A resolution are:
>
> Histogram of Rwork for models in PDB at resolution 2.10-2.30 A:
> 0.115 - 0.137 : 9 <<< you are here
> 0.137 - 0.159 : 121
> 0.159 - 0.182 : 703
> 0.182 - 0.204 : 1637
> 0.204 - 0.226 : 1749
> 0.226 - 0.248 : 735
> 0.248 - 0.270 : 147
> 0.270 - 0.293 : 12
> 0.293 - 0.315 : 2
> 0.315 - 0.337 : 2
> Histogram of Rfree for models in PDB at resolution 2.10-2.30 A:
> 0.157 - 0.181 : 20 <<< you are here
> 0.181 - 0.205 : 163
> 0.205 - 0.229 : 784
> 0.229 - 0.253 : 1733
> 0.253 - 0.277 : 1617
> 0.277 - 0.301 : 671
> 0.301 - 0.325 : 101
> 0.325 - 0.349 : 22
> 0.349 - 0.373 : 5
> 0.373 - 0.397 : 1
> Histogram of Rfree-Rwork for all model in PDB at resolution 2.10-2.30 A:
> 0.001 - 0.011 : 47
> 0.011 - 0.021 : 176
> 0.021 - 0.031 : 533
> 0.031 - 0.041 : 997 <<< you are here
> 0.041 - 0.050 : 1306
> 0.050 - 0.060 : 1062
> 0.060 - 0.070 : 602
> 0.070 - 0.080 : 216
> 0.080 - 0.090 : 113
> 0.090 - 0.100 : 65
> Number of structures considered: 5117
>
> Pavel
>
>
> On 4/3/12 9:59 AM, Christian Roth wrote:
>> Dear Phenix people,
>>
>> is there a major improvement in the algorithm? I have refined a 2.2 Ang. room
>> temperature dataset with very good data statistics (I think)
>> Rmerge 3.7%(8.9%)
>> completeness 96%(92%)
>> I/sigI 16,6(8,8)
>> in parentheses are the values for the highest resolution shell.
>>
>> After refinement I have a R/Rfree of 0.1294/0.1670.
>> In some shells there are values close to 0.100 and in the lowest shell Rfree
>> is lower than Rwork.
>> The quality of the data are really quite good, what is probably one of the
>> reasons, but I am close or below to the border of the Range of R values in
>> the pdb. Great for me, but I wanna be sure that it is really true.
>> It was a MolRep with a close homolog, but I run a torsion angle sim annealing
>> to decouple R/Rfree and the MolRep was done with an poly-Ala model to prevent
>> too much model bias.
>>
>> Best Regards
>>
>> Christian
>>
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